protocols::protein_interface_design::filters::RmsdSimpleFilter Class Reference

#include <RmsdSimpleFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::RmsdSimpleFilter:

Public Member Functions
	RmsdSimpleFilter ()
	RmsdSimpleFilter (core::Real const threshold, core::pose::PoseOP reference_pose)
bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...
protocols::filters::FilterOP	clone () const override
protocols::filters::FilterOP	fresh_instance () const override
void	report (std::ostream &out, core::pose::Pose const &pose) const override
core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...
core::Real	compute (core::pose::Pose const &pose) const
	~RmsdSimpleFilter () override
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
std::string	name () const override
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	~Filter () override
virtual std::string	get_type () const
std::string	get_user_defined_name () const
void	set_user_defined_name (std::string const &name)
virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
virtual core::Real	score (core::pose::Pose &pose)
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	class_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	superposition_transform (core::Size natoms, ObjexxFCL::FArray1_double const &weights, ObjexxFCL::FArray2_double &ref_coords, ObjexxFCL::FArray2_double &coords, numeric::xyzMatrix< core::Real > &RotM, numeric::xyzVector< core::Real > &TvecA, numeric::xyzVector< core::Real > &TvecB) const
	Superposition_transform wrapper (as in Alex Ford code protocols/toolbox/superimpose.[cc,hh]) More...
core::Real	rmsd_bb (core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB) const
	Function that performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Uses a reference to the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses. More...
core::Real	dist_bb (core::pose::Pose const &poseA, utility::vector1< core::Size > const &positions_to_alignA, core::pose::Pose const &poseB, utility::vector1< core::Size > const &positions_to_alignB) const
	Returns the BB distance of two poses respect to indexes. More...

Private Attributes
core::Real	threshold_
core::pose::PoseCOP	reference_pose_
core::Size	target_chain_
core::Size	do_align_
bool	b_target_chain_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

RmsdSimpleFilter() [1/2]

protocols::protein_interface_design::filters::RmsdSimpleFilter::RmsdSimpleFilter

(

)

RmsdSimpleFilter() [2/2]

protocols::protein_interface_design::filters::RmsdSimpleFilter::RmsdSimpleFilter	(	core::Real const	threshold,
		core::pose::PoseOP	reference_pose
	)

References reference_pose_, and threshold_.

~RmsdSimpleFilter()

protocols::protein_interface_design::filters::RmsdSimpleFilter::~RmsdSimpleFilter ( )

overridedefault

Member Function Documentation

apply()

bool protocols::protein_interface_design::filters::RmsdSimpleFilter::apply ( core::pose::Pose const &  pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), threshold_, and protocols::protein_interface_design::filters::TR().

class_name()

std::string protocols::protein_interface_design::filters::RmsdSimpleFilter::class_name ( )

static

Referenced by protocols::protein_interface_design::filters::RmsdSimpleFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdSimpleFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::compute

(

core::pose::Pose const &

pose

)

const

References b_target_chain_, core::pose::Pose::conformation(), dist_bb(), do_align_, core::conformation::Conformation::num_chains(), reference_pose_, rmsd_bb(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), target_chain_, and protocols::protein_interface_design::filters::TR().

Referenced by apply(), report(), and report_sm().

dist_bb()

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::dist_bb ( core::pose::Pose const &  poseA, utility::vector1< core::Size > const &  positions_to_alignA, core::pose::Pose const &  poseB, utility::vector1< core::Size > const &  positions_to_alignB  ) const

private

Returns the BB distance of two poses respect to indexes.

References core::pose::Pose::residue(), protocols::cluster::calibur::RMSD(), and core::conformation::Residue::xyz().

Referenced by compute().

fresh_instance()

protocols::filters::FilterOP protocols::protein_interface_design::filters::RmsdSimpleFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

name()

std::string protocols::protein_interface_design::filters::RmsdSimpleFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::protein_interface_design::filters::RmsdSimpleFilter::parse_my_tag ( utility::tag::TagCOP  , basic::datacache::DataMap &    )

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References b_target_chain_, do_align_, reference_pose_, core::pose::saved_native_pose(), core::pose::saved_reference_pose(), target_chain_, threshold_, and protocols::protein_interface_design::filters::TR().

provide_xml_schema()

void protocols::protein_interface_design::filters::RmsdSimpleFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References protocols::rosetta_scripts::attributes_for_saved_reference_pose(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::protein_interface_design::filters::RmsdSimpleFilterCreator::provide_xml_schema().

report()

void protocols::protein_interface_design::filters::RmsdSimpleFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

report_sm()

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::report_sm ( core::pose::Pose const &  ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

rmsd_bb()

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::rmsd_bb ( core::pose::Pose const &  poseA, utility::vector1< core::Size > const &  positions_to_alignA, core::pose::Pose const &  poseB, utility::vector1< core::Size > const &  positions_to_alignB  ) const

private

Function that performs alignment of the protein BB on the selected aminoacids. Returns the RMSD, Uses a reference to the rotation Matrix and Translation Vector, Will fail if both poses are not protein <-This can be fixed by adding a list of the atoms to align to the function, but I am not doing it now. Will fail if the number of residues to align is not the same in the two poses.

References core::pose::Pose::residue(), protocols::cluster::calibur::RMSD(), superposition_transform(), and core::conformation::Residue::xyz().

Referenced by compute().

superposition_transform()

void protocols::protein_interface_design::filters::RmsdSimpleFilter::superposition_transform ( core::Size  natoms, ObjexxFCL::FArray1_double const &  weights, ObjexxFCL::FArray2_double &  ref_coords, ObjexxFCL::FArray2_double &  coords, numeric::xyzMatrix< core::Real > &  RotM, numeric::xyzVector< core::Real > &  TvecA, numeric::xyzVector< core::Real > &  TvecB  ) const

private

Superposition_transform wrapper (as in Alex Ford code protocols/toolbox/superimpose.[cc,hh])

References protocols::simple_filters::coords(), protocols::toolbox::fit_centered_coords(), and protocols::toolbox::reset_x().

Referenced by rmsd_bb().

Member Data Documentation

b_target_chain_

bool protocols::protein_interface_design::filters::RmsdSimpleFilter::b_target_chain_

private

Referenced by compute(), and parse_my_tag().

do_align_

core::Size protocols::protein_interface_design::filters::RmsdSimpleFilter::do_align_

private

Referenced by compute(), and parse_my_tag().

reference_pose_

core::pose::PoseCOP protocols::protein_interface_design::filters::RmsdSimpleFilter::reference_pose_

private

Referenced by compute(), parse_my_tag(), and RmsdSimpleFilter().

target_chain_

core::Size protocols::protein_interface_design::filters::RmsdSimpleFilter::target_chain_

private

Referenced by compute(), and parse_my_tag().

threshold_

core::Real protocols::protein_interface_design::filters::RmsdSimpleFilter::threshold_

private

Referenced by apply(), parse_my_tag(), and RmsdSimpleFilter().

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The documentation for this class was generated from the following files:

• src/protocols/protein_interface_design/filters/RmsdSimpleFilter.hh
• src/protocols/protein_interface_design/filters/RmsdSimpleFilter.cc